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Systematic Biology Advance Access originally published online on September 21, 2009
Systematic Biology 2009 58(5):489-500; doi:10.1093/sysbio/syp054
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© The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Species Trees from Highly Incongruent Gene Trees in Rice

Karen A. Cranston1,2,*, Bonnie Hurwitz1,3, Doreen Ware3,4, Lincoln Stein3,5 and Rod A. Wing6,7,8

1 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
2 Biodiversity Synthesis Center, Field Museum of Natural History, Chicago, IL 60605, USA
3 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
4 Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
5 Ontario Institute for Cancer Research, Ontario, Canada M5G 0A3
6 Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721, USA
7 Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
8 BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA

* Correspondence to be sent to: Biodiversity Synthesis Center, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-mail: kcranston{at}fieldmuseum.org.


  Abstract

Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and Bayesian estimation of species trees. Our test data are a collection of genes from cultivated rice (genus Oryza) and the most closely related wild species, generated using a high-throughput sequencing protocol and bioinformatics pipeline. Trees inferred from independent genes display levels of topological incongruence that far exceed that seen in previous data sets analyzed with these species tree methods. We identify differences in phylogenetic results between inference methods that incorporate gene tree incongruence. Finally, we discuss the challenges of scaling these analyses for data sets with thousands of gene trees and extensive levels of missing data.

Keywords: Bayesian MCMC; gene tree incongruence; multilocus analysis; phylogenetic inference; rice

Received September 8, 2008; Revised November 20, 2008; Accepted August 9, 2009

Guest Associate Editor: Scott Edwards


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